Even if the methods and functions are so basic as to not have variations?

It's hard to tell about APIs, since there's no caselaw, but the rule for texts is that the smaller they are, the more original they have to be to qualify for copyright protection - so conversely, the sheer length of a work makes it more likely to be protected even if it's not that original.

So "add(a, b) returning the sum of the two" is probably not copyrightable by itself, but a whole namespace full of functions might be.

No. But the court explicitly looked at that and said that there was enough creativity in the choice of what names to give methods and how to group methods that the Java API qualifies as a creative work (and I don't think anyone would really dispute that).